cluster_analysis.py

import numpy as np
from ovito.io import import_file, export_file
from ovito.modifiers import ClusterAnalysisModifier, SelectTypeModifier, DeleteSelectedModifier
from ovito.vis import Viewport, OSPRayRenderer


def perform_cluster_analysis(input_file, particle_types, cutoff=3.0):
    """
    Performs cluster analysis on a given input file for specific particle types.

    :param input_file: Path to the input file containing particle data.
    :param particle_types: Set of particle types to include in the analysis.
    :param cutoff: Distance cutoff for cluster determination (default: 3.0).
    """
    # Import file
    pipeline = import_file(input_file)
    pipeline.add_to_scene()

    # Compute pipeline data
    data = pipeline.compute()

    # Apply SelectTypeModifier to select particles of specific types
    pipeline.modifiers.append(SelectTypeModifier(
        operate_on="particles",
        property="Particle Type",
        types=particle_types
    ))

    # Apply DeleteSelectedModifier to remove selected particles
    pipeline.modifiers.append(DeleteSelectedModifier())

    # Apply ClusterAnalysisModifier for cluster analysis
    pipeline.modifiers.append(ClusterAnalysisModifier(
        cutoff=cutoff,
        sort_by_size=True,
        cluster_coloring=True
    ))

    # Export results of the clustering algorithm to a text file
    export_file(pipeline, 'clusters.txt', 'txt/table', key='clusters')

    # Retrieve cluster information
    data = pipeline.compute()
    cluster_table = data.tables['clusters']
    print("Cluster Size:")
    print(cluster_table['Cluster Size'][...])

    # Disable cell visualization
    data.cell.vis.enabled = False

    # Configure viewport and render image
    vp = Viewport(type=Viewport.Type.Right)
    vp.zoom_all()
    vp.render_image(filename='simulation.png', size=(1000, 1000), renderer=OSPRayRenderer())


if __name__ == "__main__":
    input_file = "/path/to/your/input/file.xyz"
    particle_types = {'X'}  # Set of particle types to exclude in the analysis
    perform_cluster_analysis(input_file, particle_types)